A mobile cleaner for heat exchanger tube bundles is disclosed in commonly owned U.S. Pat. No. 5,437,296. While the prior art mobile cleaner provided an adequate cleaning of the heat exchanger tubes, it had several problems associated with its use. The first problem was that the prior art system vented some of the fumes from the cleaning solution directly into the atmosphere. Government agencies are now paying increased attention to the release of fumes into the atmosphere and have promulgated various rules and regulations concerning proper handling of vapor emissions. Another problem involved the two top doors that did not completely seal against the top of the container or with each other, allowing escape of fumes and possibly cleaning fluid. The method of cleaning with the prior art mobile unit involved transporting the cleaning fluid to the site where the cleaning would take place, cleaning, and then transporting the used cleaning material for disposal or reprocessing. The prior art mobile cleaner also required extensive set up time to change roller positions to accommodate different sized tube bundles. These and other problems associated with the prior art identify a need for a new method and system for cleaning heat exchanger tube bundles.